Sleeping Beauty mRNA-LNP enables stable rAAV transgene expression in mouse and NHP hepatocytes and improves vector potency.

Recombinant adeno-associated virus (rAAV) vector gene delivery systems have demonstrated great promise in clinical trials but continue to face durability and dose-related challenges. Unlike rAAV gene therapy, integrating gene addition approaches can provide curative expression in mitotically active cells and pediatric populations. We explored a novel in vivo delivery approach based on an engineered transposase, Sleeping Beauty (SB100X), delivered as an mRNA within a lipid nanoparticle (LNP), in combination with an rAAV-delivered transposable transgene. This combinatorial approach achieved correction of ornithine transcarbamylase deficiency in the neonatal Spfash mouse model following a single delivery to dividing hepatocytes in the newborn liver. Correction remained stable into adulthood, while a conventional rAAV approach resulted in a return to the disease state. In non-human primates, integration by transposition, mediated by this technology, improved gene expression 10-fold over conventional rAAV-mediated gene transfer while requiring 5-fold less vector. Additionally, integration site analysis confirmed a random profile while specifically targeting TA dinucleotides across the genome. Together, these findings demonstrate that transposable elements can improve rAAV-delivered therapies by lowering the vector dose requirement and associated toxicity while expanding target cell types.

Inertial Measurement Unit and Heart Rate Monitoring to Assess Cardiovascular Fitness of Manual Wheelchair Users during the Six-Minute Push Test.

Manual wheelchair users (MWUs) are prone to a sedentary life that can negatively affect their physical and cardiovascular health, making regular assessment important to identify appropriate interventions and lifestyle modifications. One mean of assessing MWUs' physical health is the 6 min push test (6MPT), where the user propels themselves as far as they can in six minutes. However, reliance on observer input introduces subjectivity, while limited quantitative data inhibit comprehensive assessment. Incorporating sensors into the 6MPT can address these limitations. Here, ten MWUs performed the 6MPT with additional sensors: two inertial measurement units (IMUs)-one on the wheelchair and one on the wrist together with a heart rate wristwatch. The conventional measurements of distance and laps were recorded by the observer, and the IMU data were used to calculate laps, distance, speed, and cadence. The results demonstrated that the IMU can provide the metrics of the traditional 6MPT with strong significant correlations between calculated laps and observer lap counts (r = 0.947, p < 0.001) and distances (r = 0.970, p < 0.001). Moreover, heart rate during the final minute was significantly correlated with calculated distance (r = 0.762, p = 0.017). Enhanced 6MPT assessment can provide objective, quantitative, and comprehensive data for clinicians to effectively inform interventions in rehabilitation.

Frameshift Mutations in Leukemia-Associated Genes Correlate With Superior Outcomes in Patients Undergoing Allogeneic Stem Cell Transplant for De Novo Acute Myeloid Leukemia.

Background: Allogeneic stem cell transplant (allo-SCT) is a mainstay of treatment for acute myeloid leukemia (AML). Its success depends largely on response of donor T lymphocytes against leukemia cells, known as graft-vs-leukemia (GvL) effect. A key potential driver of GvL is immune response to mutation-derived neoantigens. Previous studies in solid tumors have demonstrated enhanced immunogenicity of frameshift (FS)-derived peptides vs. those from non-synonymous single nucleotide variants (SNVs). We therefore hypothesized that AML cases bearing FS mutations in leukemia-associated genes would be more immunogenic than those with only other types of mutations (non-FS), and thus benefit more from allo-SCT via more robust GvL. Methods: We identified AML patients who had undergone allo-SCT between 2010 and 2022 and had next-generation sequencing data available on diagnostic specimens using a 42-gene hot spot panel. We compared the impact of tumor mutations present at diagnosis on overall survival and relapse-free survival based on FS versus non-FS status. Results: Ninety-five AML allo-SCT patients were identified. We observed superior relapse-free survival (P = 0.038, hazard ratio (HR): 0.24) and borderline superior overall survival (P = 0.058, HR: 0.55) post-transplant in de novo AML patients, who had at least one FS mutation (other than NPM1) in one of the 42 assessed genes versus those with only non-FS mutations. Conclusions: Our findings suggest that FS-mutated AML cases may benefit more from allo-SCT than those with only non-FS mutations, possibly due to increased generation of immunogenic neoepitopes. If validated in an expanded study, incorporation of somatic FS mutation status in AML could improve patient selection algorithms for bone marrow transplant and thereby lead to superior outcomes.

Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap).

Proteins undergo reversible S-acylation via a thioester linkage in vivo. S-palmitoylation, modification by C16:0 fatty acid, is a common S-acylation that mediates critical protein-membrane and protein-protein interactions. The most widely used S-acylation assays, including acyl-biotin exchange and acyl resin-assisted capture, utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. These assays generally require >500 µg of protein input material per sample and numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome these limitations, we devised "Acyl-Trap", a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S-acyl enrichment. We show that the method is compatible with protein-level detection of S-acylated proteins (e.g., H-Ras) as well as S-acyl site identification and quantification using "on trap" isobaric labeling and LC-MS/MS from as little as 20 µg of protein input. In mouse brain, Acyl-Trap identified 279 reported sites of S-acylation and 1298 previously unreported putative sites. Also described are conditions for long-term hydroxylamine storage, which streamline the assay. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional protein detection and chemoproteomic workflows.

Impacts of a herring gull colony on runoff water quality from an urban green roof.

Green infrastructure (GI) strategies, including green roofs, have become a common, decentralized, nature-based strategy for reducing urban runoff and restoring ecosystem services to the urban environment. In this study, we examined the water quality of incident rainfall and runoff from a green roof installed on top of the Jacob K. Javits Convention Center in New York City. Since the 2014 installation of this green roof, one of the largest in North America, a colony of nesting herring gulls grew to approximately 100 nesting pairs in 2018 and 150 nesting pairs in 2019. Water quality monitoring took place between September 2018 and October 2019. Except for phosphorus on some occasions, we found concentrations of nitrate, nitrite, chlorine, sulfate to be below federal drinking water standards. Levels of the fecal indicator bacteria (FIB), total coliform, E. coli, and Enterococcus, were consistently higher in runoff samples than rainwater, ranging from 150 to over 20,000 CFU/100 mL for E. coli and 100 to over 140,000 CFU/100 mL for total coliform. Quantitative polymerase chain reaction (qPCR) methods were used to search for potential opportunistic pathogens, including Legionella spp., Mycobacterium spp., Campylobacter spp., and Salmonella spp. Discovery of the presence of Catellicoccus marimammalium, a gull-associated marker in runoff water indicates that herring gulls are the likely source of contamination. Due to habitat loss, herring gulls, and other Larus gull species are increasingly nesting on urban roofs, both green (such as at the Javits Center) and conventional (such as on Rikers and Governors Islands). Habitat creation is one of the target ecosystem services desired from GI systems. Although the discharge from the green roof of the Javits Center is directed to the city's sewer system, this study demonstrates the need to treat runoff from green roofs with nesting gull populations if its intended use involves reuse or human contact.

Characteristics and Outcomes of Patients With Spina Bifida in Texas by Patient Age.

INTRODUCTION: Spina bifida (SB) occurs in 3.5/10,000 live births and is associated with significant long-term neurologic and urologic morbidity. We explored the characteristics and outcomes of pediatric patients with SB and the facilities that treat them in Texas. METHODS: We retrospectively reviewed a statewide hospital inpatient discharge database (2013-2021) to identify patients aged <18 y with SB using International Classification of Diseases 9/10 codes. Patients transferred to outside hospitals were excluded to avoid double-counting. Descriptive statistics and chi-square test were performed. RESULTS: Seven thousand five hundred thirty one inpatient hospitalizations with SB were analyzed. Most SB care is provided by a few facilities. Two facilities (1%) averaged >100 SB admissions per year (33% of patients), while 15 facilities (8%) treat 10-100 patients per year (51% of patients). Most facilities (145/193, 75%) average less than one patient per year. Infants tended to be sicker (17% extreme illness severity, P < 0.001). Overall mortality is low (1%), primarily occurring in the neonatal period (8%, P < 0.001). Most admissions are associated with surgical intervention, with 63% of encounters having operating room charges with an average cost of $25,786 ± 24,884. Admissions for spinal procedures were more common among infants, whereas admissions for genitourinary procedures were more common among older patients (P < 0.001). The average length of stay was 8 ± 16 d with infants having the longest length of stay (19 ± 33, P < 0.001). CONCLUSIONS: Patients have significant long-term health needs with evolving pediatric surgical indications as they grow. Pediatric SB care is primarily provided by a small number of facilities in Texas. Longitudinal care coordination of their multidisciplinary surgical care is needed to optimize patient care.

Grazing herbivores reduce herbaceous biomass and fire activity across African savannas.

Fire and herbivory interact to alter ecosystems and carbon cycling. In savannas, herbivores can reduce fire activity by removing grass biomass, but the size of these effects and what regulates them remain uncertain. To examine grazing effects on fuels and fire regimes across African savannas, we combined data from herbivore exclosure experiments with remotely sensed data on fire activity and herbivore density. We show that, broadly across African savannas, grazing herbivores substantially reduce both herbaceous biomass and fire activity. The size of these effects was strongly associated with grazing herbivore densities, and surprisingly, was mostly consistent across different environments. A one-zebra increase in herbivore biomass density (~100 kg/km2 of metabolic biomass) resulted in a ~53 kg/ha reduction in standing herbaceous biomass and a ~0.43 percentage point reduction in burned area. Our results indicate that fire models can be improved by incorporating grazing effects on grass biomass.

Machine Learning the Disorder Landscape of Majorana Nanowires.

We develop a practical machine learning approach to determine the disorder landscape of Majorana nanowires by using training of the conductance matrix and inverting the conductance data in order to obtain the disorder details in the system. The inversion carried out through machine learning using different disorder parametrizations turns out to be unique in the sense that any input tunnel conductance as a function of chemical potential and Zeeman energy can indeed be inverted to provide the correct disorder landscape. Our work opens up a qualitatively new direction of directly determining the topological invariant and the Majorana wave-function structure corresponding to a transport profile of a device using simulations that quantitatively match the specific conductance profile. In addition, this also opens up the possibility for optimizing Majorana systems by figuring out the (generally unknown) underlying disorder only through the conductance data. An accurate estimate of the applicable spin-orbit coupling in the system can also be obtained within the same scheme.

Versatile luminescence thermometry via intense green defect emission from an infrared-pumped fluorosilicate optical fiber.

An all-glass optical fiber capable of two distinct methods of optical thermometry is described. Specifically, a silica-clad, barium fluorosilicate glass core fiber, when pumped in the infrared, exhibits visibly intense green defect luminescence whose intensity and upper-state lifetime are strong functions of temperature. Intensity-based optical thermometry over the range from 25°C to 130°C is demonstrated, while a lifetime-based temperature sensitivity is shown from 25°C to 100°C. Time-domain measurements yield a relative sensitivity of 2.85% K -1 at 373 K (100°C). A proof-of-concept distributed sensor system using a commercial digital single-lens reflex camera is presented, resulting in a measured maximum relative sensitivity of 1.13% K -1 at 368 K (95°C). The sensing system described herein stands as a new blueprint for defect-based luminescence thermometry that takes advantage of pre-existing and relatively inexpensive optical components, and allows for the use of standard cameras or simply direct human observation.

A Prolonged Case of Severe Mpox as an Opportunistic Infection in Advanced AIDS.

The case report discusses a 29-year-old male with advanced HIV who experienced one of the longest, confirmed cases of monkeypox (mpox) infection. Despite treatment with antivirals and supportive care, including intravenous tecovirimat and vaccinia immune globulin, the patient's condition worsened over a six-and-a-half-month period. He suffered from widespread ulcerative, necrotic lesions and multiple complications, including acute kidney injury, multi-drug resistant bacterial infections, and respiratory failure. Despite repeated treatments, including brincidofovir, the patient remained PCR-positive for monkeypox virus (MPXV) with low cycle threshold (Ct) values, indicating active infection. The case underscores the severity of mpox in immunocompromised individuals, particularly those with advanced HIV, and highlights the challenges in managing such cases. The patient's persistently low CD4 count and unsuppressed HIV viral load likely contributed to the inability to clear the virus. The report emphasizes the need for further research to optimize treatment strategies for MPXV infection, especially in people living with HIV.

Disproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency.

Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed carbon-use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in Pseudomonas putida, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our 13C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent 13C-metabolic flux analysis revealed a 3-fold lower investment of sugar carbons in CO2 efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis revealed enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO2-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained the substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided perspective for predicting the microbial conversion of accessible organic matter to CO2 efflux.

Super-Obesity is Associated With an Increased Risk of Complications Following Primary Total Knee Arthroplasty.

BACKGROUND: Obesity, defined as a body mass index (BMI) ≥ 30, is an ever-growing epidemic, with > 35% of adults in the United States currently classified as obese. Super-obese individuals, defined as those who have a BMI ≥ 50, are the fastest-growing portion of this group. This study sought to quantify the infection risk as well as the incidence of surgical, medical, and thromboembolic complications among super-obese patients undergoing total knee arthroplasty (TKA). METHODS: An all-payer claims database was used to identify patients who underwent elective, primary TKA between 2016 and 2021. Patients who had a BMI ≥ 50 were compared to those who had a normal BMI of 18 to 25. Demographics and the incidence of 90-days postoperative complications were compared between the 2 groups. Univariate analysis and multivariable regression were used to assess differences between groups. RESULTS: In total, 3,376 super-obese TKA patients were identified and compared to 17,659 patients who had a normal BMI. Multivariable analysis indicated that the super-obese cohort was at an increased postoperative risk of periprosthetic joint infection (adjusted odds ratio [aOR] 3.7, 95% confidence interval [CI]: 2.1 to 6.4, P < .001), pulmonary embolism (aOR 2.2, 95%-CI: 1.0 to 5.0, P = .047), acute respiratory failure (aOR 4.1, 95%-CI: 2.7 to 6.1, P < .001), myocardial infarction (aOR 2.5, 95%-CI: 1.1 to 5.8, P = .026), wound dehiscence (aOR 2.3, 95%-CI: 1.4 to 3.8, P = .001), and acute renal failure (aOR 3.2, 95%-CI: 2.4 to 4.2, P < .001) relative to patients who have normal BMI. CONCLUSIONS: Super-obese TKA patients are at an elevated risk of postoperative infectious, surgical, medical, and thromboembolic complications. As such, risk stratification, as well as appropriate medical management and optimization, is of utmost importance for this high-risk group.

Inhibition of the eukaryotic initiation factor-2-α kinase PERK decreases risk of autoimmune diabetes in mice.

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress-responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eIF2α. In T1D, maladaptive unfolded protein response (UPR) in insulin-producing beta cells renders these cells susceptible to autoimmunity. We found that inhibition of the eIF2α kinase PERK, a common component of the UPR and ISR, reversed the mRNA translation block in stressed human islets and delayed the onset of diabetes, reduced islet inflammation, and preserved ß cell mass in T1D-susceptible mice. Single-cell RNA sequencing of islets from PERK-inhibited mice showed reductions in the UPR and PERK signaling pathways and alterations in antigen processing and presentation pathways in ß cells. Spatial proteomics of islets from these mice showed an increase in the immune checkpoint protein PD-L1 in ß cells. Golgi membrane protein 1, whose levels increased following PERK inhibition in human islets and EndoC-ßH1 human ß cells, interacted with and stabilized PD-L1. Collectively, our studies show that PERK activity enhances ß cell immunogenicity, and inhibition of PERK may offer a strategy to prevent or delay the development of T1D.

LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations.

Generating simulation-ready molecular models for the LAMMPS molecular dynamics (MD) simulation software package is a difficult task and impedes the more widespread and efficient use of MD in materials design and development. Fixed-bond force fields generally require manual assignment of atom types, bonded interactions, charges, and simulation domain sizes. A new LAMMPS pre- and postprocessing toolkit (LUNAR) is presented that efficiently builds molecular systems for LAMMPS. LUNAR automatically assigns atom types, generates bonded interactions, assigns charges, and provides initial configuration methods to generate large molecular systems. LUNAR can also incorporate chemical reactivity into simulations by facilitating the use of the REACTER protocol. Additionally, LUNAR provides postprocessing for free volume calculations, cure characterization calculations, and property predictions from LAMMPS thermodynamic outputs. LUNAR has been validated via building and simulation of pure epoxy and cyanate ester polymer systems with a comparison of the corresponding predicted structures and properties to benchmark values, including experimental results from the literature. LUNAR provides the tools for the computationally driven development of next-generation composite materials in the Integrated Computational Materials Engineering (ICME) and Materials Genome Initiative (MGI) frameworks. LUNAR is written in Python with the usage of NumPy and can be used via a graphical user interface, a command line interface, or an integrated design environment. LUNAR is freely available via GitHub.

Inhibition of the Eukaryotic Initiation Factor-2-α Kinase PERK Decreases Risk of Autoimmune Diabetes in Mice.

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress-responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eIF2α. In T1D, maladaptive unfolded protein response (UPR) in insulin-producing ß cells renders these cells susceptible to autoimmunity. We show that inhibition of the eIF2α kinase PERK, a common component of the UPR and ISR, reverses the mRNA translation block in stressed human islets and delays the onset of diabetes, reduces islet inflammation, and preserves ß cell mass in T1D-susceptible mice. Single-cell RNA sequencing of islets from PERK-inhibited mice shows reductions in the UPR and PERK signaling pathways and alterations in antigen processing and presentation pathways in ß cells. Spatial proteomics of islets from these mice shows an increase in the immune checkpoint protein PD-L1 in ß cells. Golgi membrane protein 1, whose levels increase following PERK inhibition in human islets and EndoC-ßH1 human ß cells, interacts with and stabilizes PD-L1. Collectively, our studies show that PERK activity enhances ß cell immunogenicity, and inhibition of PERK may offer a strategy to prevent or delay the development of T1D.

Homeocurvature adaptation of phospholipids to pressure in deep-sea invertebrates.

Hydrostatic pressure increases with depth in the ocean, but little is known about the molecular bases of biological pressure tolerance. We describe a mode of pressure adaptation in comb jellies (ctenophores) that also constrains these animals' depth range. Structural analysis of deep-sea ctenophore lipids shows that they form a nonbilayer phase at pressures under which the phase is not typically stable. Lipidomics and all-atom simulations identified phospholipids with strong negative spontaneous curvature, including plasmalogens, as a hallmark of deep-adapted membranes that causes this phase behavior. Synthesis of plasmalogens enhanced pressure tolerance in Escherichia coli, whereas low-curvature lipids had the opposite effect. Imaging of ctenophore tissues indicated that the disintegration of deep-sea animals when decompressed could be driven by a phase transition in their phospholipid membranes.

Heme pocket modulates protein conformation and diguanylate cyclase activity of a tetrameric globin coupled sensor.

Bacteria use the second messenger cyclic dimeric guanosine monophosphate (c-di-GMP) to control biofilm formation and other key phenotypes in response to environmental signals. Changes in oxygen levels can alter c-di-GMP signaling through a family of proteins termed globin coupled sensors (GCS) that contain diguanylate cyclase domains. Previous studies have found that GCS diguanylate cyclase activity is controlled by ligand binding to the heme within the globin domain, with oxygen binding resulting in the greatest increase in catalytic activity. Herein, we present evidence that heme-edge residues control O2-dependent signaling in PccGCS, a GCS protein from Pectobacterium carotovorum, by modulating heme distortion. Using enzyme kinetics, resonance Raman spectroscopy, small angle X-ray scattering, and multi-wavelength analytical ultracentrifugation, we have developed an integrated model of the full-length PccGCS tetramer and have identified conformational changes associated with ligand binding, heme conformation, and cyclase activity. Taken together, these studies provide new insights into the mechanism by which O2 binding modulates activity of diguanylate cyclase-containing GCS proteins.

Factors influencing intraoperative conversion from double- to single-incision mastectomy with free nipple grafts in 352 transgender and non-binary patients.

BACKGROUND: Double-incision mastectomy (DIM) with free nipple grafts (FNG) is a common technique employed in gender-affirming mastectomy (GAM), but is associated with a high scar burden. Intraoperatively, the surgeon may opt for a single-incision mastectomy (SIM) along the inframammary folds (IMF) to optimize aesthetic outcomes. This study sought to identify factors predictive of intraoperative conversion. METHODS: From February 2018 to November 2022, TGNB patients who underwent GAM at a single institution were retrospectively reviewed. Data regarding patient characteristics, perioperative details, postoperative complications, and aesthetic satisfaction were collected. RESULTS: A total of 352 patients were identified. Median age and body mass index (BMI) were 25.0 years (IQR: 9.0) and 28.5 kg/m2 (IQR: 8.5), respectively. Most patients received IMF incisions (n = 331, 94.0%); of whom, 66 (19.9%) underwent intraoperative conversion from DIM to SIM with FNG. Larger breast cup-size (p < 0.001) and a greater degree of ptosis (p = 0.002) preoperatively were significantly associated with intraoperative conversion to SIM. There was no significant association between intraoperative conversion and the ratio of intermammary distance to the width of the chest wall (p = 0.086). Overall complication rates were significantly higher among patients with diabetes mellitus (p = 0.015) and a greater degree of ptosis (p = 0.018). 77.8% (n = 274) of patients were satisfied with their aesthetic outcome. NPWT usage was associated with higher rates of aesthetic satisfaction (83.6% vs. 77.8%; p = 0.005). CONCLUSION: Patients with larger breast cup size and greater degree of ptosis should be counseled preoperatively that they may be at a higher risk of conversion to a singular incision.